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for file in $(<list.txt)
do
join_paired_ends.py -f ${file}F_sub.fastq -r ${file}R_sub.fastq -o ${file}/
mv ${file}/fastqjoin.join.fastq Merged_Reads/${file}_merged.fastq
convert_fastaqual_fastq.py -c fastq_to_fastaqual -f Merged_Reads/${file}_merged.fastq -o Merged_Reads/${file}
mv Merged_Reads/${file}/${file}_merged.fna Merged_Reads/${file}_merged.fasta
rm -r Merged_Reads/${file}
rm Merged_Reads/${file}_merged.fastq
rm -r ${file}/
done
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